Index

A

AccProxGrad (class in mushi.optimization) ancom() (in module mushi.composition) arrays() (eta method), [1] (History method) (mu method), [1]

as_df() (kSFS method)

C

C() (in module mushi.utils) centralize() (in module mushi.composition) check_grid() (eta method), [1] (History method) (mu method), [1] clear_eta() (kSFS method)

clear_mu() (kSFS method) closure() (in module mushi.composition) clr() (in module mushi.composition) clr_inv() (in module mushi.composition) clustermap() (kSFS method) (mu method), [1]

D

dkl() (in module mushi.loss_functions)

E

epochs() (eta method), [1] (History method) (mu method), [1]

eta (class in mushi) (class in mushi.histories) (kSFS attribute) (kSFS property)

F

f() (AccProxGrad method) (LineSearcher method) (Optimizer method) (ThreeOpProxGrad method) (TrendFilter method)

fold() (in module mushi.utils)

H

History (class in mushi.histories)

I

ilr() (in module mushi.composition) ilr_inv() (in module mushi.composition) infer_eta() (kSFS method)

infer_misid() (kSFS method) infer_mush() (kSFS method) inner() (in module mushi.composition)

K

kSFS (class in mushi)

L

LineSearcher (class in mushi.optimization)

loss() (kSFS method) lsq() (in module mushi.loss_functions)

M

M() (in module mushi.utils) misid_partners() (in module mushi.utils) module mushi.composition mushi.histories mushi.loss_functions mushi.optimization mushi.utils mu (class in mushi) (class in mushi.histories) (kSFS attribute) (kSFS property)

multiplicative_replacement() (in module mushi.composition) mushi.composition module mushi.histories module mushi.loss_functions module mushi.optimization module mushi.utils module mutation_types (kSFS attribute) mutype_misid() (in module mushi.utils)

N

n (kSFS attribute)

O

Optimizer (class in mushi.optimization)

P

perturb() (in module mushi.composition) perturb_inv() (in module mushi.composition) plot() (eta method), [1] (History method) (kSFS method) (mu method), [1]

plot_cumulative() (mu method), [1] plot_total() (kSFS method) power() (in module mushi.composition) prf() (in module mushi.loss_functions)

R

revcomp() (in module mushi.utils) run() (AccProxGrad method) (LineSearcher method) (Optimizer method) (ThreeOpProxGrad method) (TrendFilter method)

S

set_eta() (kSFS method)

simulate() (kSFS method)

T

ThreeOpProxGrad (class in mushi.optimization) tmrca_cdf() (kSFS method)

tmrca_sf() (in module mushi.utils) TrendFilter (class in mushi.optimization)

X

X (kSFS attribute)

x (Optimizer attribute)

Y

y (eta property), [1]

Z

Z (mu property), [1]